Alzheimer's disease (AD) continues to progress despite decades of research on protein aggregation, highlighting the need to understand upstream homeostatic failures. Among the earliest alterations in AD are disruptions of circadian rhythms and autophagy, which are mechanistically intertwined. Although circadian dysfunction and autophagic failure have been studied separately, the stage-dependent, region-specific, and cell-type-specific interplay between these systems remains poorly integrated, limiting the development of targeted interventions. In a healthy brain, the circadian clock and autophagy mutually interact, maintaining proteostasis, neuronal function, and rhythmic metabolic and immune processes. In early-stage AD, circadian rhythms show mild disruption and autophagy initiation remains active, but downstream autophagosome-lysosome fusion and lysosomal degradation are impaired, leading to the accumulation of AD pathological proteins. Dysregulation is cell-type-specific: neuronal clocks remain relatively intact, whereas astrocytic and microglial clocks exhibit altered metabolic and immune rhythms, contributing to early pathogenic events. In late-stage AD, severe circadian disruption likely uncouples circadian control from autophagy, and these dysfunctions mutually exacerbate each other, driving neuroinflammation, neuronal dysfunction, and further accumulation of pathological proteins. This review synthesizes current evidence on the circadian-autophagy axis, highlighting mechanistic insights and therapeutic opportunities, and emphasizes the importance of integrating stage-, region-, and cell-type-specific dynamics for the development of precise interventions in AD.

Cytosolic NAD□ synthesis supports ovarian cancer growth by enabling PARP16-dependent mono(ADP-ribosyl)ation (MARylation) of ribosomal proteins, thereby fine-tuning translation and maintaining protein homeostasis. While genetic depletion of PARP16 disrupts ribosome MARylation and impairs tumor cell growth, the therapeutic potential of pharmacologic PARP16 inhibition in this pathway remains unexplored. Here, we characterized the effects of DB008, a tool compound that functions as a selective inhibitor of PARP16, in ovarian cancer cells. Biochemical analyses demonstrated that PARP16 undergoes NAD□-dependent auto-MARylation and that NMNAT-2 supplies NAD□ to support this activity. DB008 potently inhibited PARP16 auto-MARylation in vitro. In ovarian cancer cells, DB008 engaged PARP16, reduced its MARylation, and decreased ribosome-associated MARylation. Consistent with PARP16 depletion, DB008 enhanced global protein synthesis, increased protein aggregation, and suppressed cell growth and anchorage-independent colony formation. CRISPR-mediated deletion of the PARP16 gene in ovarian cancer cells abolished the effects of DB008 on translation, protein aggregation, and proliferation, demonstrating on-target activity. Moreover, cells expressing a PARP16 mutant resistant to DB008 were unaffected by inhibitor treatment, further confirming that the cellular effects of DB008 require on-target inhibition. Finally, DB008 significantly inhibited tumor growth in OVCAR3 xenografts, with on-target engagement of PARP16 in the xenograft tumors. Collectively, these findings establish PARP16 as a druggable regulator of ribosome MARylation and protein homeostasis in ovarian cancer and provide pharmacologic proof-of-concept that disrupting ribosomal MARylation impairs tumor growth.

Protein aggregation remains a major challenge in biopharmaceutical development, despite extensive efforts to mitigate this process. Mechanical stresses, such as shaking, promote aggregation through interface-mediated pathways. During shaking, proteins are simultaneously exposed to three types of interfaces, air-liquid, solid-liquid, and air-liquid-solid; however, the relative contribution of each interface to aggregation remains unresolved. In this report, we systematically evaluated the disruption of protein aggregates at the glass vial surface by shear flow generated during shaking. Computational fluid dynamics was used to estimate shear rates at the vial surface under shaking conditions that increase the amount of protein aggregates. The shear rate, along with a harsher shear condition, was then applied to protein-coated glass vial surfaces using a gyroscopic mixer. Importantly, the vials were filled with buffer solution to eliminate contributions from the air-liquid and air-liquid-solid interfaces. Under these controlled conditions, no increase in protein aggregation was detected, indicating that shear-mediated disruption of protein films by shear flow at the solid-liquid interface plays only a minor role in protein aggregation. Complementary shaking experiments with headspace showed no measurable aggregation attributable to the air-liquid-solid interface. These findings identify the air-liquid interface as the dominant contributor to protein aggregation during shaking. This study clarifies the mechanistic role of individual interfaces in shake-induced protein aggregation and offers practical guidance for formulation design, container-filling strategies, and process conditions to minimize protein aggregation in biopharmaceutical products.

A hallmark of Neurodegenerative Diseases (NDs) is protein misfolding, aggregation, and accumulation in specific brain regions. The accumulation of insoluble, misfolded protein aggregates is usually referred to as amyloid formation. This process leads to cellular dysfunction, destruction of neurons, loss of neuronal connections in specific brain areas, and brain damage. Despite the involvement of distinct pathogenic proteins, the underlying mechanisms of misfolding and aggregate formation are remarkably similar across various NDs. In this review, we present a comprehensive overview of the medicinal chemistry and mechanistic insights into phytochemicals and synthetic small molecules with potential for the treatment of neurodegenerative disorders. Various small molecules have been reported to have therapeutic effects by inhibiting the misfolding, aggregation, and accumulation of pathogenic proteins, such as amyloid-β, tau, and α- synuclein. This review mainly covers natural product-derived small molecules, notably polyphenols (including flavonoids and non-flavonoid polyphenols), as well as other phytochemical classes, such as quinones and alkaloids, along with their possible mechanisms of action. In addition, synthetic small molecules, osmolytes, metal chelators, and repurposed drugs for neurodegenerative disorders are thoroughly discussed.

Neurodegenerative disorders are marked by progressive deterioration of neurons, affecting cognitive, memory, and motor functions. This decline creates substantial personal and social challenges, making early identification of risk factors essential for effective intervention. Environmental toxicants, such as chemicals and air pollutants, are suspected to negatively impact brain health. This review critically examines the relationship between environmental toxicants and neurodegenerative disorders, exploring their potential mechanisms and providing recommendations for future research. A PubMed search was performed for all available data until April 2024 using keywords related to environmental toxicants and neurodegenerative diseases. The search was limited to peer-reviewed articles in English, focusing on human studies that investigate the association between toxicants and neurodegenerative disorders. A narrative synthesis was conducted based on the neurodegenerative disorder, specific toxicants, and mechanisms of action. This review highlights the detrimental effects of chemical toxicants and air pollutants on diseases, such as Parkinson's, Alzheimer's, multiple sclerosis, and Huntington's disease. Key mechanisms discussed include oxidative stress, protein aggregation, and mitochondrial dysfunction. The findings emphasize the need to understand the mechanisms by which environmental toxicants contribute to neurodegenerative diseases. Early detection and management, including reduced exposure to harmful substances, are vital. Further research is essential for improving screening techniques and developing targeted interventions.

Cryo-electron microscopy (cryo-EM) is the only technique capable of visualizing the lipid bilayer of extracellular vesicles (EVs), enabling their distinction from non-EV particles. However, the application of cryo-EM for EV sample characterization has been limited by a combination of low imaging throughput and complex image analysis of the structurally diverse EVs. To address these challenges, we developed a workflow combining automated cryo-EM image acquisition with supervised machine learning (sML)-assisted particle detection and classification. Automated image acquisition facilitates the routine acquisition of thousands of cryo-EM images with consistent quality, enabling the imaging of hundreds of EVs. sML-assisted particle detection enabled efficient and reproducible identification, size measurement, and structural classification of EVs. Furthermore, using sML we are able to differentiate EVs from non-EV particles, such as lipoproteins and protein aggregates, which might co-isolate due to overlapping physical properties or by physical association with EVs. In mixed EV-lipoprotein samples, we demonstrate that our pipeline can distinguish EVs and differentiate between high-density (HDL), low-density (LDL), and very low-density (VLDL) lipoproteins. Our automated cryo-EM and sML workflow overcomes key limitations of EV characterization using cryo-EM by increasing imaging throughput and enabling reproducible EV characterization. Furthermore, this method provides a tool for analysing EV heterogeneity, sample purity, and co-isolated contaminants, advancing the field of EV research.

Protein aggregation and transmission are hallmarks of neurodegenerative diseases. Praja1 E3 ubiquitin ligase has been shown to suppress the aggregation of causative proteins in amyotrophic lateral sclerosis, frontotemporal lobar degeneration, Parkinson's disease, Huntington's disease, and spinocerebellar degeneration, which include transactivation response DNA-binding protein of 43 kDa, fused in sarcoma, superoxide dismutase 1, α-synuclein, huntingtin, and ataxin-3. Aoki etal. demonstrated that Praja1 ubiquitinates and degrades tau, a key molecule in tauopathies such as Alzheimer's disease, Pick's disease, progressive supranuclear palsy, and corticobasal syndrome, furthering our understanding of the role of Praja1 in neurodegenerative diseases and potential therapeutic approaches.

Persistent pathological structures, such as tumors, fibrotic nodules, granulomas, microbial biofilms, or protein aggregates, are traditionally viewed as age-related conditions that emerge after reproduction, when natural selection is less effective at eliminating traits expressed late in life. However, some pathologies with robust and organized architectures can arise surprisingly early, challenging this classical perspective. We recently proposed that intra-organismal selection for function, a selective process operating within organisms and acting on non-reproducing entities by favoring structural configurations that enhance stability, robustness, and novelty generation, may play a role in aging. Here, we suggest that this same process can also operate well before the so-called selection shadow (i.e., life stages where natural selection is too weak to purge deleterious mutations). We identify three non-mutually exclusive mechanisms that may promote this early-life action: (i) initial local adaptive benefits, such as improved tissue repair or containment of infection; (ii) limited or context-specific fitness costs, allowing structurally stable but abnormal configurations to persist undetected; and (iii) rapid environmental changes that reshape tissue-level selective landscapes, driven by pollutants, endocrine disruptors, or novel diets. Recognizing early-onset organized pathologies as by-products of eco-evolutionary tissue dynamics, rather than as mere developmental errors, reframes their biological significance and opens new therapeutic avenues. Instead of targeting cells exclusively, future strategies could focus on disrupting the functional architecture of pathological tissues and structures, offering novel means to prevent or control early-life diseases shaped by internal selection forces.

CryAB-driven amyloidogenesis in Drosophila muscle engages extracellular vesicle pathways for cellular release.

Protein aggregation: at the origins of neurodegenerative diseases

Recent advances in small molecules for amyloid fibril inhibition: chemical strategies and molecular mechanistic insights from lysozyme and insulin models.

METTL18 ensures pancreatic function by maintaining proper translation and proteostasis.

Impact of starch surface hydrophobicity on gluten aggregation behavior in dough-like model systems.

Alzheimer disease (AD) is a degenerative disorder of the central nervous system. Its main pathological feature is the formation of neurofibrillary tangles through abnormal β-amyloid protein (Aβ) aggregation and excessive Tau protein phosphorylation. Ring finger and WD repeating domain 2 (RFWD2) is an E3 ubiquitin ligase that regulates neuronal dendrite complexity through the c-Jun N-terminal kinase (JNK) pathway. This study aimed to investigate the regulatory effect of RFWD2 on the downstream protein, serum/glucocorticoid-regulated kinase 1 (SGK1), through the JNK pathway and explore its influence on AD pathogenesis. Cognitive-level behavioral detection was performed in RFWD2+/- mice. Cultured PC12 cells and cortical neurons were also used to analyze the changes in signaling pathways caused by the decreased expression of RFWD2 invitro and correlations between the expression of related proteins and key signaling pathways of AD at the molecular level. Decreased RFWD2 expression led to cognitive deficits in AD mice, resulting in mitochondrial swelling, fragmentation of hippocampal neurons, abnormally high reactive oxygen species levels, and an imbalance between antiapoptotic and proapoptotic proteins. This effect was significantly improved by inhibiting the JNK pathway and SGK1 protein expression. Furthermore, invitro experiments showed that in PC12 cells and cortical neurons downregulated by RFWD2, the expression levels of p-JNK, SGK1, and p-Tau increased, and those of LC3B/Beclin-1 decreased; ROS levels increased, and apoptosis was induced; inhibiting JNK or SGK1 expression reversed these changes. RFWD2 regulates SGK1 expression through the JNK pathway, thereby regulating mitochondrial autophagy and apoptosis, altering the expression levels of p-Tau and Aβ proteins, inducing AD-like symptoms in mice, and promoting AD development. The RFWD2-JNK-SGK1 axis provides a valuable basis for studying the mechanisms of AD occurrence and developing early intervention strategies.

Neurofilament light chain protein exposure contributes to protein aggregation, microgliosis, astrogliosis and neuroinflammation via p38/MK2/NF-κB/CREB1/Nrf2/HO-1 signalling leading to Parkinson's disease.

Mechanistic studies on glycinin basic subunit/soybean soluble polysaccharide complexes: Ionic modulation and implications for soy sauce secondary precipitate.

cGAS-STING activation in Parkinson's Disease: From mechanisms to Disease-Modifying therapeutic strategies.

The olfactory nerve possesses unique anatomical features, including direct central nervous system (CNS) projection and continuous regeneration. Scientific advances have elucidated mechanisms such as combinatorial receptor coding and signal amplification. This review summarizes these foundations and examines olfactory dysfunction in COVID-19 and Parkinson's disease (PD). In COVID-19, evidence suggests that SARS-CoV-2 targets sustentacular cells rather than olfactory neurons, causing gene downregulation and parosmia attributed to incomplete peripheral filtering, while direct CNS invasion remains rare. In PD, olfactory loss is a prodromal feature. However, seed amplification assays reveal that alpha-synuclein aggregation in the nasal mucosa does not fully correlate with olfactory dysfunction, as reflected by differences between PD and Multiple System Atrophy. This, together with correlations with cardiac sympathetic denervation, challenges simple pathogen propagation hypotheses. We propose that PD-related hyposmia reflects a systemic vulnerability involving deficits in energy metabolism and neural network organization, rather than solely peripheral protein aggregation. Understanding these pathologies requires a multifaceted approach beyond anatomical lesions.

Mechanistic insight into polysaccharides and ultrasound synergistic enhancement of the quality of low-salt surimi gels

Autophagy dysregulation has been implicated in the toxic protein aggregates of amyotrophic lateral sclerosis (ALS). However, the causal relationship between impaired autophagy and ALS remains ambiguous, necessitating further elucidation. This Mendelian randomization (MR) study employs a two-sample design, utilizing genetic instruments to proxy autophagy dysregulation as the exposure and ALS as the outcome. It incorporates summary statistics of ALS (27,205 cases, 110,881 controls), along with data on DNA methylation, RNA splicing, gene expression, and protein abundance quantitative trait loci (QTLs) in both blood and brain tissues (mQTL, sQTL, eQTL, and pQTL, respectively) sourced from European cohorts. Cis-variants situated proximal to or within the 604 autophagy-related genes, exhibiting robust associations with molecular alterations in autophagy, are employed as instrumental variables. Their causal links with ALS are assessed via summary-data-based MR (SMR) analyses, followed by Bayesian colocalization, sensitivity analyses, brain cell-specific MR analyses, protein-protein interaction (PPI), and druggable analyses. Consistent evidence supported the causal effects of two lysosome genes (FNBP1 and IDUA), one autophagy core gene (C9orf72), and one mitophagy gene (USP35) on ALS risk. Specifically, brain FNBP1 splicing level (OR = 1.18, p = 3.38E-5) and blood USP35 expression level (OR = 1.17, p = 5.94E-5) were positively associated with higher ALS risk. In contrast, we found strong causal evidence of brain IDUA methylation level (OR = 0.96, p = 8.36E-6) and blood C9orf72 methylation level (OR = 0.55, p = 7.59E-12) with lower ALS risk. Cell-type-specific MR analyses, PPI, and druggable analyses further nominated the key brain cell type (astrocytes), potential interaction with known causative genes (SQSTM1 and PFN1), and promising druggability for FNBP1 in ALS. This multi-omics MR study identified causal associations between the regulation of four autophagy-related genes and ALS risk, shedding light on autophagy-mediated mechanisms and offering early evidence of novel therapeutic targets for ALS.